Yes, that's what I was reading. But as @Kyriakos876 commented that he had found a workaround, I thought it had worked for him.

A workaround would be the following: you have to create a variable (I named it IsExplorer) which will be set to 1 if Explorer is focused and to 0 if it's not. For this you need an IfMatch option. Add it to the [FullscreenCheck] measure, replacing the existing IfCondition:

See that I kept the IfActions and replaced the IfCondition with the above IfMatch. The appropriate IfMatchAction / IfNotMatchAction set the value of IsExplorer variable to 1 if Explorer is focused and to 0, if it's not. The check isn't case sensitive (due to the (?i) operator).
Now the action needed to be executed can be executed by a new Calc measure, which you have to add:

A workaround would be the following: you have to create a variable (I named it IsExplorer) which will be set to 1 if Explorer is focused and to 0 if it's not. For this you need an IfMatch option. Add it to the [FullscreenCheck] measure, replacing the existing IfCondition:

See that I kept the IfActions and replaced the IfCondition with the above IfMatch. The appropriate IfMatchAction / IfNotMatchAction set the value of IsExplorer variable to 1 if Explorer is focused and to 0, if it's not. The check isn't case sensitive (due to the (?i) operator).
Now the action needed to be executed can be executed by a new Calc measure, which you have to add:

[Rainmeter]
Update=3000
; Lines beginning with a semicolon are code comments.
; They are here to help you understand the functions in this skin.
; Checks for fullscreen once every three seconds.
; If you paste a part of this skin into another, be sure that it updates at a reasonable rate.
; Too slow and it will be slow to toggle your skins.
; Too fast and it will drain resources unnecessarily.
; 1000-10000 is a reasonable range.
[Metadata]
Author=rockhevy1000
Information=This is a fork of GlobTwo's FullScreenSwitch skin, that uses JSMorley's IsFullScreen plugin to switch skins on and off during gaming. Or fullscreen Youtube. Or anything running in fullscreen, really. In the original code when you are in the desktop or click in the wallpaper, the plugin detects the process Explorer.EXE as a fullscreen and deactivate the skins. The improve is a workaround to this issue. Also, helps if you want to blacklist certain process of your PC. Thanks to the rainmeter's community for the support and help with the codding. Edit the skin, in the code, are the instructions about what you have to do to make it work.
; You can cut and paste the section below into any skin, but it must stay open during fullscreen. In other words, don't put this into a skin you intend to automatically turn off.
[FullscreenCheck]
Measure=Plugin
Plugin=IsFullScreen
IfEqualValue=1
; Here is where you specify which skins to activate/deactivate. Be sure to add skins to both this list and the activation list below. Check your skins folders for the correct names.
IfEqualAction=[!DeactivateConfig "Simple Epoca\Clock][!DeactivateConfig "A dock"][!DeactivateConfig "Simple Epoca\Player"][!DeactivateConfig "Simple Epoca\Weather"][!DeactivateConfig "TranslucentTaskbar"][!DeactivateConfig "Enmon\Visualizer]
IfBelowValue=1
; And to turn skins back on when not in fullscreen:
IfBelowAction=[!ActivateConfig "Simple Epoca\Clock"][!ActivateConfig "A dock"][!ActivateConfig "Simple Epoca\Player"][!ActivateConfig "Simple Epoca\Weather"][!ActivateConfig "TranslucentTaskbar"][!ActivateConfig "Enmon\Visualizer]
; Here is where you specify which process to blacklist. You need to create another IfMatch and his actions and variables. Be sure to no conflict between them.
IfMatch=(?i)Explorer.EXE
IfMatchAction=[!SetVariable IsExplorer "1"]
IfNotMatchAction=[!SetVariable IsExplorer "0"]
[IsExplorerScreen]
Measure=Calc
; Here is where you specify the variables. You need to put the name in the Formula=.
Formula=( FullscreenCheck * #IsExplorer# )
IfCondition=(#CURRENTSECTION#>=1)
; Here is where you specify which skins are maintained activated. You can copy the list in the IfBelowAction= to make it easier
IfTrueAction=[!ActivateConfig "Simple Epoca\Clock"][!ActivateConfig "A dock"][!ActivateConfig "Simple Epoca\Player"][!ActivateConfig "Simple Epoca\Weather"][!ActivateConfig "TranslucentTaskbar"][!ActivateConfig "Enmon\Visualizer]
DynamicVariables=1
; End cut and paste.
[String]
Meter=String

Hello, this is what you mean? The code of the skin was thus finally. And I didn't do anything, just click on the desktop.

Yep, that's needed, however I don't know what to say, because I can't replicate the issue. Using the original code, posted into the first post of this topic by jsmorely, if I click the desktop, the skin says Desktop, not Explorer. Still don't know what are you doing, to get the skin to return Explorer.EXE.

Yep, that's needed, however I don't know what to say, because I can't replicate the issue. Using the original code, posted into the first post of this topic by jsmorely, if I click the desktop, the skin says Desktop, not Explorer. Still don't know what are you doing, to get the skin to return Explorer.EXE.

Like I say it before, maybe is a problem related to Windows itself. I checked my code and the jsmorely's code so many times and the plugins keep saying me Explorer.exe.
Also, check the plugin version and it's ok.

And this is the errorSyntax error: IfCondition=(FullscreenCheck=1) && (0 <> "Explorer.EXE")

Do you (or anyone) has and idea what I'm doing wrong?

Sorry for the late reply and confusion. I see the issue has been resolved but I just want to make myself clear for future references:
As you and Jsmorley said this should and does throw and error for the mentioned reasons. I later figured it out as well and added the [FullscreenCheck:] result in a variable and then check if THAT matches with "Explorer.exe" in a different measure. If it does, it creates a variable with the value of 1 that is the actual variable for the IfCondition along with the FullscreenCheck which is already a number. I edited my first post to avoid future confusion.

Hello, I created an account to mention that I'm also having this issue where IsFullScreen 3.0 detects desktop as fullscreen and the "FullscreenSwitch" skin unloads my other skins whenever I click on desktop.